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Fusarium oxysporum vs Magnaporthe poae LastZ results

Fusarium oxysporum (Fusarium oxysporum f. sp. lycopersici, FO2) and Magnaporthe poae (Magnaporthe poae ATCC 64411, Mag_poae_ATCC_64411_V1) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Fungi release 110. Fusarium oxysporum was used as the reference species. After running LastZ, the raw LastZ alignment blocks were chained according to their location in both genomes. During the final netting process, the best sub-chain was chosen in each region on the reference species.

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91

Chunking parameters

ParameterFusarium oxysporumMagnaporthe poae
Chunk size10,000,00010,100,000
Overlap0100,000
Group set size10,100,00010,100,000
Masking options

Statistics over 22,041 alignment blocks

Genome coverage (bp) Coding exon coverage (bp)
Fusarium oxysporum

Uncovered: 48,608,648 out of 61,470,697
Covered: 12,862,049 out of 61,470,697

Uncovered: 11,746,339 out of 21,631,774
Matches: 5,984,559 out of 21,631,774
Mismatches: 3,658,745 out of 21,631,774
Insertions: 242,131 out of 21,631,774
Identity over aligned base-pairs: 60.5%

Magnaporthe poae

Uncovered: 28,870,487 out of 39,503,331
Covered: 10,632,844 out of 39,503,331

Uncovered: 6,647,604 out of 14,559,232
Matches: 5,008,290 out of 14,559,232
Mismatches: 2,561,913 out of 14,559,232
Insertions: 341,425 out of 14,559,232
Identity over aligned base-pairs: 63.3%

Block size distribution

Size range All 22,041 alignment blocks Blocks grouped in nets
# blocks Total size (incl. gaps) # nets Total size (incl. gaps)
1 bp - 10 bp
47
264.0 bp
10 bp - 100 bp
2,349
156.3 kb
471
33.4 kb
100 bp - 1 kb
15,499
6.3 Mb
4,324
2.1 Mb
1 kb - 10 kb
4,119
7.4 Mb
4,042
9.9 Mb
10 kb - 100 kb
27
548.9 kb
149
2.5 Mb